Variant report

Variant	rs4888270
Chromosome Location	chr16:74698576-74698577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:74698291-74699444	GM12892	blood:	n/a	n/a
2	POLR2A	chr16:74698567-74699228	GM12892	blood:	n/a	n/a
3	POLR2A	chr16:74697170-74699187	GM12891	blood:	n/a	n/a
4	POLR2A	chr16:74697007-74699353	K562	blood:	n/a	n/a
5	POLR2A	chr16:74697046-74699481	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:74698468-74699314	K562	blood:	n/a	n/a
7	POLR2A	chr16:74698494-74699260	K562	blood:	n/a	n/a
8	POLR2A	chr16:74698445-74699398	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr16:74698417-74699714	GM12878	blood:	n/a	n/a
10	POLR2A	chr16:74698470-74699579	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr16:74698546-74699027	MCF-7	breast:	n/a	n/a
12	POLR2A	chr16:74698538-74699081	GM12891	blood:	n/a	n/a
13	POLR2A	chr16:74698409-74698620	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:74698318-74699705	GM12892	blood:	n/a	n/a
15	HEY1	chr16:74697140-74700066	K562	blood:	n/a	n/a
16	POLR2A	chr16:74698171-74699322	GM12892	blood:	n/a	n/a
17	POLR2A	chr16:74697564-74700009	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:74698571-74698621	BE2_C	brain:	n/a
2	chr16:74698571-74698621	GM12891	blood:	n/a
3	chr16:74698571-74698621	U87	brain:	n/a
4	chr16:74698571-74698621	SAEC	small airway:	n/a
5	chr16:74698571-74698621	IMR90	lung:	fetal
6	chr16:74698571-74698621	SK-N-MC	brain:	n/a
7	chr16:74698571-74698621	NB4	blood:	n/a
8	chr16:74698571-74698621	PrEC	prostate:	n/a
9	chr16:74698571-74698621	HCPEpiC	choroid plexus:	n/a
10	chr16:74698571-74698621	Hela-S3	cervix:	n/a
11	chr16:74698571-74698621	NHDF-neo	bronchial:	n/a
12	chr16:74698571-74698621	HCM	heart:	n/a
13	chr16:74698571-74698621	HPAEpiC	pulmonary alveolar:	n/a
14	chr16:74698571-74698621	K562	blood:	n/a
15	chr16:74698571-74698621	HRCEpiC	kidney:	n/a
16	chr16:74698571-74698621	AG04449	skin:	fetal
17	chr16:74698571-74698621	GM19239	blood:	n/a
18	chr16:74698571-74698621	HCF	heart:	n/a
19	chr16:74698571-74698621	HNPCEpiC	eye:	n/a
20	chr16:74698571-74698621	ECC-1	luminal epithelium:	n/a
21	chr16:74698571-74698621	AG04450	lung:	fetal
22	chr16:74698571-74698621	HMEC	breast:	n/a
23	chr16:74698571-74698621	HRE	kidney:	n/a
24	chr16:74698571-74698621	Hepatocyte	liver:	n/a
25	chr16:74698571-74698621	NHBE	bronchial:	n/a
26	chr16:74698571-74698621	T-47D	breast:	n/a
27	chr16:74698571-74698621	CMK	blood:	n/a
28	chr16:74698571-74698621	HEK293	kidney:	embryo
29	chr16:74698571-74698621	Jurkat	blood:	n/a
30	chr16:74698571-74698621	PANC-1	pancreas:	n/a
31	chr16:74698571-74698621	MCF10A-Er-Src	breast:	n/a
32	chr16:74698571-74698621	NT2-D1	testis:	n/a
33	chr16:74698571-74698621	HUVEC	blood vessel:	n/a
34	chr16:74698571-74698621	GM12878	blood:	n/a
35	chr16:74698571-74698621	MCF-7	breast:	n/a
36	chr16:74698571-74698621	AG10803	skin:	n/a
37	chr16:74698571-74698621	PFSK-1	brain:	n/a
38	chr16:74698571-74698621	NH-A	brain:	n/a
39	chr16:74698571-74698621	GM06990	blood:	n/a
40	chr16:74698571-74698621	AoSMC	blood vessel:	n/a
41	chr16:74698571-74698621	AG09309	skin:	n/a
42	chr16:74698571-74698621	A549	lung:	n/a
43	chr16:74698571-74698621	BJ	skin:	n/a
44	chr16:74698571-74698621	SKMC	muscle:	n/a
45	chr16:74698571-74698621	HAEpiC	amniotic membrane:	n/a
46	chr16:74698571-74698621	AG09319	gingival:	n/a
47	chr16:74698571-74698621	H1-hESC	embryonic stem cell:	embryo
48	chr16:74698571-74698621	ovcar-3	ovarian:	n/a
49	chr16:74698571-74698621	HCT-116	colon:	n/a
50	chr16:74698571-74698621	SK-N-SH_RA	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:74657630..74659377-chr16:74696166..74698749,2	K562	blood:
2	chr16:74695152..74698756-chr16:74699147..74702582,8	MCF-7	breast:
3	chr16:74660349..74663096-chr16:74695955..74699046,3	MCF-7	breast:
4	chr16:74695853..74699155-chr16:74725334..74728139,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MLKL-3	chr16:74698233-74698643	NONHSAT143699

No data

Variant related genes	Relation type
ENSG00000262904	TF binding region
ENSG00000262904	CpG island
ENSG00000262904	Chromatin interaction
ENSG00000168411	Chromatin interaction
ENSG00000168404	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10400930	0.87[ASN][1000 genomes]
rs12921903	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12935075	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13339156	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28377859	0.88[ASN][1000 genomes]
rs28502731	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4072222	0.96[ASN][1000 genomes]
rs4072450	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4243108	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4271617	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4286131	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4287593	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4302071	0.87[ASN][1000 genomes]
rs4344772	0.82[ASN][1000 genomes]
rs4462623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4548905	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4564599	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4588013	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887776	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887777	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887779	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888257	0.80[ASN][1000 genomes]
rs4888258	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888259	0.86[ASN][1000 genomes]
rs4888266	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57488599	0.96[ASN][1000 genomes]
rs58136167	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6564145	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6564146	0.84[ASN][1000 genomes]
rs6564147	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564148	0.86[ASN][1000 genomes]
rs6564149	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564152	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6564153	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6564154	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6564155	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564157	0.92[ASN][1000 genomes]
rs7184754	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7185722	0.88[ASN][1000 genomes]
rs7190631	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7193423	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193508	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193583	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7193959	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7194687	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7195135	0.83[ASN][1000 genomes]
rs7195499	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7196369	0.80[ASN][1000 genomes]
rs7196627	0.83[EUR][1000 genomes]
rs7204382	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7204804	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7205258	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7342732	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047243	0.83[ASN][1000 genomes]
rs8047523	0.83[EUR][1000 genomes]
rs8048596	0.82[ASN][1000 genomes]
rs8049056	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8050615	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8050624	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052923	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8053084	0.84[ASN][1000 genomes]
rs8055784	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8055803	0.83[ASN][1000 genomes]
rs8056718	0.86[ASN][1000 genomes]
rs8057279	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8058034	0.87[ASN][1000 genomes]
rs8058437	0.83[ASN][1000 genomes]
rs8058922	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8062404	0.86[ASN][1000 genomes]
rs8062959	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9921672	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9925807	0.84[ASN][1000 genomes]
rs9927073	0.83[ASN][1000 genomes]
rs9928181	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9929483	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9931225	0.94[ASN][1000 genomes]
rs9938833	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	esv275138	chr16:74647795-74722907	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv2760414	chr16:74647795-74741615	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
8	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
9	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	nsv572975	chr16:74677312-74702254	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4888270	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4888270	RFWD3	cis	Thyroid	GTEx
rs4888270	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4888270	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs4888270	RFWD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:74678600-74699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr16:74685000-74700000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr16:74685800-74699400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr16:74687200-74699800	Weak transcription	Right Atrium	heart
14	chr16:74688000-74699200	Strong transcription	Placenta	Placenta
15	chr16:74688000-74699400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr16:74689000-74698800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:74689200-74699600	Strong transcription	Fetal Intestine Small	intestine
18	chr16:74689200-74699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr16:74689400-74699200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:74689600-74699200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr16:74689800-74699600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr16:74690000-74699400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr16:74690200-74699000	Strong transcription	Fetal Brain Female	brain
24	chr16:74690600-74698800	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr16:74690600-74699000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:74690600-74699000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr16:74690800-74699000	Strong transcription	Osteobl	bone
28	chr16:74691600-74699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr16:74691600-74699200	Strong transcription	Fetal Lung	lung
30	chr16:74691600-74699200	Strong transcription	NH-A	brain
31	chr16:74692000-74699200	Strong transcription	Ovary	ovary
32	chr16:74692000-74699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr16:74692000-74699400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr16:74692200-74699200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr16:74692400-74698800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr16:74692400-74698800	Strong transcription	Lung	lung
37	chr16:74692400-74698800	Strong transcription	HUVEC	blood vessel
38	chr16:74692400-74699000	Strong transcription	Adipose Nuclei	Adipose
39	chr16:74692400-74699800	Weak transcription	Stomach Mucosa	stomach
40	chr16:74692600-74699000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:74692600-74699000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:74692600-74699000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr16:74692600-74699400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr16:74692800-74698800	Strong transcription	Liver	Liver
45	chr16:74692800-74699000	Strong transcription	Brain Anterior Caudate	brain
46	chr16:74692800-74700400	Transcr. at gene 5' and 3'	Dnd41	blood
47	chr16:74693000-74699000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:74693200-74699000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr16:74693200-74699200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr16:74693400-74699000	Strong transcription	Spleen	Spleen

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